Updated

A civilian appeals court has now reversed the verdicts of the only two Guantanamo Bay prisoners convicted in trials by military tribunal, casting a shadow over proceedings set to resume this week at the U.S. base in Cuba for the men accused in the Sept. 11 terrorist attack.

A federal appeals court on Friday threw out the military commission conviction of Ali Hamza al-Bahlul, who was charged with providing material support to terrorism and conspiracy for making propaganda videos for al-Qaida. That followed the dismissal in October of the conviction of Salim Hamdan, a driver for Osama bin Laden.

Al-Bahlul and Hamdan were the only prisoners convicted in a trial by the tribunals known as a military commission. The five other convictions of Guantanamo prisoners came through plea bargains.

There are two pending death penalty cases at Guantanamo: one against a prisoner accused of orchestrating the attack on the USS Cole in 2000, the other against five men accused of planning and aiding the Sept. 11 terrorist attacks. But the recent reversals have raised new questions about the use of military commissions in complex terrorism cases.

"The fact that no conviction can stand up on appeal does not bode well for the military commission system," said James Connell, a lawyer for Ammar al-Baluchi, a Pakistani who is one of the five charged in the Sept. 11 attacks.

The U.S. Court of Appeals for the District of Columbia Circuit on Friday overturned al-Bahlul's November 2008 conviction. In October, the court overturned Hamdan's August 2008 conviction. In both cases, the reasoning was the same.

The court determined that before enactment of the Military Commissions Act of 2006, which authorized the tribunals for the terrorism suspects at Guantanamo, only violations of the international law of war and pre-existing federal offenses were subject to trial by military commission, a special court for wartime offenses. The court said the charges of material support for terrorism and conspiracy did not meet that standard.

The Justice Department let the deadline to appeal the Hamdan ruling expire, perhaps because he has already been released after serving his 5 ½ year sentence and is back home in Yemen with his family. But the government said it disagreed with the ruling in court papers and is likely to challenge the al-Bahlul ruling.

A Pentagon spokesman, Army Lt. Col. Todd Breasseale, said "the al-Bahlul ruling has no bearing on the substantive merits," of the Sept. 11 case, which will be the subject of a four-day pretrial hearing scheduled to start Monday.

But the reversals hang like a cloud over the proceedings since the Sept. 11 case is vastly more complex than al-Bahlul or Hamdan, which were portrayed by officials at the time as warm-ups to the more significant prosecutions.

"It just shows just how shaky the entire military commission system is," said Andrea Prasow, an attorney for Human Rights Watch who was part of the defense team when Hamdan was convicted at Guantanamo in August 2008.

The cases couldn't be much more different. Hamdan was a relatively minor figure, dismissed as a "small player," even by the military judge who presided over his trial. Al-Bahlul, now serving life at Guantanamo, didn't even mount a defense.

The Sept. 11 case features five defendants facing the death penalty for charges that include nearly 3,000 counts of murder for their alleged roles in planning and helping orchestrate the worst terrorist attack on U.S. soil. Their May 5 arraignment was an unruly 13-hour spectacle, drawn out as the defendants refused to use the court translation system and ignored the judge, and any eventual conviction would face a multitude of appeals.

"Men's lives are on the line," Prasow said. "I think that's all the more reason for the government to proceed very cautiously and make sure that it is confident that it has a firm legal basis upon which to pursue these charges."

Already, the Hamdan and al-Bahlul cases are creating confusion in the Sept. 11 case.

The chief prosecutor for the Guantanamo tribunals, Army Brig. Gen. Mark Martins, sought to withdraw the charge of conspiracy in the Sept. 11 case, leaving seven charges against them.

"There are significant litigation risks attendant to proceeding with the joint conspiracy charge as a separate and stand-alone offense in the subject case," Martins said in a motion released Friday.

But then his recommendation to withdraw the charge was overruled by Convening Authority Bruce MacDonald, a retired admiral who oversees the military commissions, who said the conspiracy charge was still under judicial review.

The debate over the conspiracy charge won't be at issue at this week's hearing. A judge set the four-day proceeding at the base hear arguments on about two dozen defense and prosecution motions that must be resolved prior to a trial that is likely at least a year away.

Among the motions is one from lawyers for the five defendants, who include self-professed terrorist mastermind Khalid Sheikh Mohammed, requiring the U.S. government to preserve the secret overseas prisons where the men were held, and subjected to harsh interrogations, before they were taken to Guantanamo. Those prisons, they argue, are potential evidence for claims that the prisoners were subjected to torture.